Index

_

__init__() (cubats.slide_collection.slide.Slide method) (cubats.slide_collection.slide_collection.SlideCollection method) _plot_segmentation_on_tissue() (in module cubats.slide_collection.segmentation) _process_single_tile() (in module cubats.slide_collection.tile_colocalization)

_process_three_tiles() (in module cubats.slide_collection.tile_colocalization) _process_two_tiles() (in module cubats.slide_collection.tile_colocalization) _segment_file() (in module cubats.slide_collection.segmentation) _segment_tile() (in module cubats.slide_collection.segmentation)

A

antigen_profile (cubats.slide_collection.slide.Slide attribute)

C

calculate_percentage_and_score() (in module cubats.slide_collection.tile_quantification) collection_info_df (cubats.slide_collection.slide_collection.SlideCollection attribute)

collection_list (cubats.slide_collection.slide_collection.SlideCollection attribute) colocalization_dir (cubats.slide_collection.slide_collection.SlideCollection attribute) color_deconvolution() (in module cubats.slide_collection.tile_quantification)

D

dab_tile_dir (cubats.slide_collection.slide.Slide attribute) data_dir (cubats.slide_collection.slide_collection.SlideCollection attribute)

dest_dir (cubats.slide_collection.slide_collection.SlideCollection attribute) detailed_quantification_results (cubats.slide_collection.slide.Slide attribute) dual_antigen_expressions (cubats.slide_collection.slide_collection.SlideCollection attribute)

E

evaluate_antigen_pair() (cubats.slide_collection.slide_collection.SlideCollection method) evaluate_antigen_pair_tile() (in module cubats.slide_collection.tile_colocalization) evaluate_antigen_triplet() (cubats.slide_collection.slide_collection.SlideCollection method)

evaluate_antigen_triplet_tile() (in module cubats.slide_collection.tile_colocalization) evaluate_staining_intensities() (in module cubats.slide_collection.tile_quantification) extract_mask_tile_coordinates() (cubats.slide_collection.slide_collection.SlideCollection method)

G

generate_antigen_pair_combinations() (cubats.slide_collection.slide_collection.SlideCollection method)

generate_antigen_triplet_combinations() (cubats.slide_collection.slide_collection.SlideCollection method)

I

is_mask (cubats.slide_collection.slide.Slide attribute)

is_reference (cubats.slide_collection.slide.Slide attribute)

L

level_count (cubats.slide_collection.slide.Slide attribute)

level_dimensions (cubats.slide_collection.slide.Slide attribute)

M

mask (cubats.slide_collection.slide_collection.SlideCollection attribute) mask_coordinates (cubats.slide_collection.slide_collection.SlideCollection attribute)

mask_tile() (in module cubats.slide_collection.tile_quantification) masked_tiles (cubats.slide_collection.slide.Slide attribute)

N

name (cubats.slide_collection.slide.Slide attribute) (cubats.slide_collection.slide_collection.SlideCollection attribute)

O

openslide_object (cubats.slide_collection.slide.Slide attribute)

P

pickle_dir (cubats.slide_collection.slide_collection.SlideCollection attribute)

properties (cubats.slide_collection.slide.Slide attribute)

Q

quantification_results (cubats.slide_collection.slide_collection.SlideCollection attribute) quantification_summary (cubats.slide_collection.slide.Slide attribute) quantify_all_slides() (cubats.slide_collection.slide_collection.SlideCollection method)

quantify_single_slide() (cubats.slide_collection.slide_collection.SlideCollection method) quantify_slide() (cubats.slide_collection.slide.Slide method) quantify_tile() (in module cubats.slide_collection.tile_quantification)

R

reconstruct_dir (cubats.slide_collection.slide_collection.SlideCollection attribute) reconstruct_slide() (cubats.slide_collection.slide.Slide method) register_slides() (cubats.slide_collection.slide_collection.SlideCollection method) (in module cubats.slide_collection.registration)

register_slides_high_resolution() (in module cubats.slide_collection.registration) register_slides_with_reference() (in module cubats.slide_collection.registration) run_tumor_segmentation() (in module cubats.slide_collection.segmentation)

S

Slide (class in cubats.slide_collection.slide) SlideCollection (class in cubats.slide_collection.slide_collection)

src_dir (cubats.slide_collection.slide_collection.SlideCollection attribute) summarize_quantification_results() (cubats.slide_collection.slide.Slide method)

T

tile_count (cubats.slide_collection.slide.Slide attribute) tiles (cubats.slide_collection.slide.Slide attribute)

tiles_dir (cubats.slide_collection.slide_collection.SlideCollection attribute) triplet_antigen_results (cubats.slide_collection.slide_collection.SlideCollection attribute) tumor_segmentation() (cubats.slide_collection.slide_collection.SlideCollection method)